Contacts of the helix formed by residues 117 - 136 (chain A) in PDB entry 7JDW
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with LYS 117 (chain A).
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
85A ASN* 5.3 6.3 + - - +
114A TYR* 4.1 37.3 - - + -
115A PHE 3.0 11.9 + - - +
116A PRO* 1.3 69.2 - - - +
118A ASP* 1.3 65.0 + - - +
120A LEU* 3.8 15.1 - - + +
121A LYS* 3.0 25.5 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASP 118 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 4.1 12.1 - - - +
117A LYS* 1.3 76.5 + - - +
119A HIS* 1.3 73.1 + - - +
121A LYS* 3.5 9.6 + - - +
122A LYS* 3.2 43.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with HIS 119 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
116A PRO* 3.1 21.7 + - + +
118A ASP* 1.3 84.8 - - - +
120A LEU* 1.3 67.7 + - + +
122A LYS* 3.2 12.5 + - - +
123A ALA* 3.1 18.2 + - + +
349A HIS* 4.2 2.5 - + - -
350A PRO* 3.7 16.6 - - + +
352A TRP* 3.3 26.9 - + + -
397A ASN* 3.0 40.8 + - + -
400A SER* 2.9 32.8 + - - -
401A LEU* 6.1 1.1 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 120 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 4.1 26.6 - - + +
84A GLU* 6.0 0.4 - - - -
85A ASN* 4.6 6.5 - - - +
86A ALA* 4.2 25.1 - - + +
114A TYR* 4.9 2.7 - - + -
115A PHE* 3.6 34.3 - - + +
116A PRO 3.0 15.9 + - - +
117A LYS* 3.8 18.6 - - + +
118A ASP 3.4 0.2 - - - -
119A HIS* 1.3 79.8 - - + +
121A LYS* 1.3 57.4 + - - +
123A ALA* 3.0 9.1 + - + +
124A VAL* 2.9 33.4 + - + +
352A TRP* 5.7 0.9 - - + -
401A LEU* 4.2 18.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 121 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
117A LYS 3.0 17.1 + - - +
118A ASP* 3.6 10.1 - - - +
120A LEU* 1.3 76.7 - - - +
122A LYS* 1.3 61.8 + - + +
124A VAL* 3.2 12.0 + - + +
125A ALA* 3.1 21.7 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 122 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
118A ASP* 3.2 41.1 + - - +
119A HIS* 3.2 12.3 + - - +
121A LYS* 1.3 77.2 - - + +
123A ALA* 1.3 57.6 + - - +
125A ALA* 3.4 8.1 + - - +
126A GLU* 3.0 32.4 + - - +
397A ASN* 3.8 35.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 123 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 4.0 17.0 - - + -
119A HIS* 3.1 12.1 + - + +
120A LEU* 3.0 12.5 + - + +
122A LYS* 1.3 75.1 - - - +
124A VAL* 1.3 64.5 + - - +
126A GLU* 3.2 13.1 + - - +
127A ILE* 2.9 30.3 + - - +
397A ASN* 4.1 3.5 - - - +
398A ALA* 3.9 25.4 - - + +
401A LEU* 5.2 4.9 - - + -
408A TRP* 5.3 0.2 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with VAL 124 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
83A ALA* 4.1 15.5 - - + +
84A GLU* 3.8 36.3 - - + +
120A LEU* 2.9 20.7 + - + +
121A LYS* 3.2 11.4 + - + +
123A ALA* 1.3 75.2 - - - +
125A ALA* 1.3 57.2 + - - +
127A ILE* 3.2 5.3 + - - +
128A GLU* 2.9 48.6 + - + +
----------------------------------------------------------
Back to top of page
Residues in contact with ALA 125 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
121A LYS 3.1 9.3 + - - +
122A LYS* 3.5 11.4 - - - +
124A VAL* 1.3 80.1 - - - +
126A GLU* 1.3 63.5 + - + +
128A GLU* 3.3 8.1 + - - +
129A GLU* 3.1 22.6 + - - +
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 126 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
122A LYS* 3.0 19.7 + - - +
123A ALA* 3.6 6.2 - - - +
125A ALA* 1.3 76.9 - - + +
127A ILE* 1.3 58.7 + - - +
129A GLU* 3.5 7.2 + - - +
130A MET* 3.1 25.1 + - - +
393A VAL* 4.8 1.2 - - - +
394A ASN* 3.4 26.4 + - - +
395A ILE* 3.2 22.2 - - + +
396A ARG* 3.8 5.2 + - - +
397A ASN* 2.9 33.7 + - - +
398A ALA* 2.9 29.9 + - + -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 127 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.6 21.3 - - + -
81A GLY 3.8 5.2 - - - +
83A ALA* 5.6 1.8 - - + +
123A ALA 2.9 21.4 + - - +
124A VAL* 3.9 5.2 - - - +
126A GLU* 1.3 73.0 - - - +
128A GLU* 1.3 60.2 + - - +
130A MET* 3.3 20.7 + - + +
131A CYS* 3.0 27.8 + - - -
143A ARG* 3.5 25.8 - - - +
395A ILE* 4.2 8.5 - - + -
398A ALA* 3.9 16.2 - - + -
408A TRP* 3.7 40.8 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 128 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
82A ARG* 5.4 2.9 + - - -
84A GLU* 5.5 1.2 - - - +
124A VAL* 2.9 34.7 + - + +
125A ALA* 3.3 8.0 + - - +
127A ILE* 1.3 76.6 - - - +
129A GLU* 1.3 57.7 + - - +
131A CYS* 3.3 8.3 + - - +
132A ASN* 3.0 36.5 + - - +
135A LYS* 5.6 2.6 + - - -
143A ARG* 3.0 34.2 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with GLU 129 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
125A ALA 3.1 13.0 + - - +
126A GLU* 3.7 10.1 - - - +
128A GLU* 1.3 75.1 - - - +
130A MET* 1.3 60.2 + - - +
132A ASN* 3.0 24.9 + - - +
133A ILE* 2.8 56.0 + - + +
393A VAL* 5.3 4.7 - - + -
394A ASN 6.1 0.2 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with MET 130 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 4.7 8.5 - - + -
126A GLU 3.1 13.9 + - - +
127A ILE* 3.4 29.2 - - + +
129A GLU* 1.3 75.0 - - - +
131A CYS* 1.3 58.2 + - - +
133A ILE* 3.1 6.7 + - - +
134A LEU* 2.9 39.6 + - + +
363A LEU* 5.0 1.3 - - + -
371A MET* 4.0 20.8 - - - +
393A VAL* 4.3 15.2 - - + +
395A ILE* 4.6 2.5 - - + -
405A PHE* 3.8 37.9 - - + +
408A TRP* 4.7 7.6 - - + -
409A THR* 3.6 31.4 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with CYS 131 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
80A VAL* 3.7 32.3 - - - -
127A ILE 3.0 20.3 + - - -
128A GLU* 3.6 10.1 - - - +
129A GLU 3.2 0.2 - - - -
130A MET* 1.3 76.0 - - - +
132A ASN* 1.3 63.4 + - - +
134A LEU* 3.3 9.7 + - - +
135A LYS* 3.0 47.1 + - - +
141A VAL* 4.0 7.6 - - + +
143A ARG* 3.8 26.7 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with ASN 132 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 3.0 21.5 + - - +
129A GLU* 3.0 32.5 + - - +
131A CYS* 1.3 76.4 - - - +
133A ILE* 1.3 62.9 + - + +
135A LYS* 3.2 18.8 + - - +
136A THR* 3.0 23.7 + - - -
----------------------------------------------------------
Back to top of page
Residues in contact with ILE 133 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
129A GLU* 2.8 40.9 + - + +
130A MET* 3.6 7.0 - - - +
132A ASN* 1.3 76.8 - - + +
134A LEU* 1.3 56.4 + - - +
136A THR* 3.0 12.0 + - + -
137A GLU* 2.8 33.8 + - + +
371A MET* 4.1 9.4 - - + -
391A ILE* 3.8 27.4 - - + -
392A LYS 4.5 6.3 - - - +
393A VAL* 3.5 26.5 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LEU 134 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
75A LEU* 4.7 5.4 - - + -
78A VAL* 4.1 5.2 - - + -
80A VAL* 3.7 29.6 - - + -
130A MET* 2.9 35.4 + - + +
131A CYS* 3.3 7.6 + - - +
133A ILE* 1.3 75.4 - - - +
135A LYS* 1.3 64.3 + - - +
137A GLU* 2.9 12.4 + - - +
138A GLY 3.2 0.2 + - - -
139A VAL* 2.9 45.3 + - + +
141A VAL* 3.8 17.3 - - + -
363A LEU* 4.7 5.2 - - + -
365A LEU* 4.4 14.6 - - + -
371A MET* 3.9 22.9 - - + -
409A THR* 5.1 1.3 - - + -
----------------------------------------------------------
Back to top of page
Residues in contact with LYS 135 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
128A GLU* 5.6 2.8 + - - -
131A CYS* 3.0 31.4 + - - +
132A ASN* 3.2 17.1 + - - +
134A LEU* 1.3 76.0 - - - +
136A THR* 1.3 61.8 + - - +
138A GLY* 3.0 13.9 + - - -
139A VAL 3.5 16.3 + - - +
141A VAL* 3.9 28.5 - - + +
143A ARG* 6.1 0.6 - - - +
----------------------------------------------------------
Back to top of page
Residues in contact with THR 136 (chain A).
Click here for Legend to table.
----------------------------------------------------------
Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
132A ASN 3.0 15.0 + - - -
133A ILE* 3.2 16.4 - - + +
135A LYS* 1.3 79.0 - - - +
137A GLU* 1.3 70.3 + - - +
138A GLY 3.0 4.7 + - - -
----------------------------------------------------------
Back to top of page
A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
------------------------------------------------------------
Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
------------------------------------------------------------
Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il